fixed log filter error due to submission of "none" as a filter value

.gitignore

@@ -9,3 +9,9 @@ dist/
 *.egg-info/
 .pytest_cache/
 .mypy_cache/
+
+*.db
+
+*.R
+
+migrations/

DEVELOPMENT

@@ -0,0 +1,65 @@
+## How to use the logger
+
+### GUI Interactions:
+
+```python
+ActivityLog.log_gui_interaction(
+    action="view_paper_details",
+    description="User viewed paper details",
+    paper_id=123
+)
+```
+
+### Configuration Changes:
+
+```python
+ActivityLog.log_gui_interaction(
+    action="view_paper_details",
+    description="User viewed paper details",
+    paper_id=123
+)
+```
+
+### Scraper Commands:
+
+```python
+ActivityLog.log_scraper_command(
+    action="start_scraper", 
+    status="running"
+)
+```
+
+### Scraper Activities:
+
+```python
+ActivityLog.log_scraper_activity(
+    action="download_paper",
+    paper_id=123,
+    status="success",
+    description="Paper downloaded successfully",
+    file_path="/papers/123.pdf"
+)
+```
+
+### Error Logging:
+
+```python
+# Simple error
+ActivityLog.log_error(
+    error_message="Failed to connect to API",
+    severity=ErrorSeverity.WARNING.value,
+    source="api_client"
+)
+
+# Logging an exception
+try:
+    result = some_risky_operation()
+except Exception as e:
+    ActivityLog.log_error(
+        error_message="Operation failed",
+        exception=e,
+        severity=ErrorSeverity.ERROR.value,
+        source="data_processor",
+        paper_id=paper_id
+    )
+```

Makefile

@@ -1,10 +1,13 @@
 # List of phony targets (targets that don't represent files)
-.PHONY: all clean venv run format format-check lint mypy test dist reformat dev
+.PHONY: all clean venv run format format-check lint mypy test dist reformat dev celery celery-flower redis run-all
 
 # Define Python and pip executables inside virtual environment
 PYTHON := venv/bin/python
 PIP := venv/bin/pip
 
+# Celery worker command
+CELERY := venv/bin/celery
+
 # Default target that runs the application
 all: run
 
@@ -83,11 +86,11 @@ todos:
 	@grep -r "TODO\|FIXME" scipaperloader || echo "No TODOs found"
 
 # Reset the database: delete, initialize, and migrate
-reset-db:
+reset-db: venv
 	rm -f $(DB_PATH)
-	flask db init || true
-	flask db migrate -m "Initial migration"
-	flask db upgrade
+	$(PYTHON) -m flask --app scipaperloader db init || true
+	$(PYTHON) -m flask --app scipaperloader db migrate -m "Initial migration"
+	$(PYTHON) -m flask --app scipaperloader db upgrade
 
 # Create and set up virtual environment
 venv:
@@ -130,3 +133,21 @@ dist: format-check lint mypy test
 
 # Set up complete development environment
 dev: clean venv
+
+# Start Celery worker for processing tasks
+celery: venv
+	$(CELERY) -A celery_worker:celery worker --loglevel=info
+    
+# Monitor Celery tasks with flower web interface
+celery-flower: venv
+	$(PIP) install flower
+	$(CELERY) -A celery_worker:celery flower --port=5555
+
+# Check if Redis is running, start if needed
+redis:
+	@redis-cli ping > /dev/null 2>&1 || (echo "Starting Redis server..." && redis-server --daemonize yes)
+
+# Run complete application stack (Flask app + Celery worker + Redis)
+run-all: redis
+	@echo "Starting Flask and Celery..."
+	@$(MAKE) -j2 run celery

README.md

@@ -14,7 +14,8 @@ And open it in the browser at [http://localhost:5000/](http://localhost:5000/)
 
 ## Prerequisites
 
-Python >=3.8
+- Python >=3.8
+- Redis (for Celery task queue)
 
 ## Development environment
 
@@ -40,12 +41,44 @@ Python >=3.8
    add development dependencies under `project.optional-dependencies.*`; run
    `make clean && make venv` to reinstall the environment
 
+## Asynchronous Task Processing with Celery
+
+SciPaperLoader uses Celery for processing large CSV uploads and other background tasks. This allows the application to handle large datasets reliably without blocking the web interface.
+
+### Running Celery Components
+
+- `make redis`: ensures Redis server is running (required for Celery)
+
+- `make celery`: starts a Celery worker to process background tasks
+
+- `make celery-flower`: starts Flower, a web interface for monitoring Celery tasks at http://localhost:5555
+
+- `make run-all`: runs the entire stack (Flask app + Celery worker + Redis) in development mode
+
+### How It Works
+
+When you upload a CSV file through the web interface:
+
+1. The file is sent to the server
+2. A Celery task is created to process the file asynchronously
+3. The browser shows a progress bar with real-time updates
+4. The results are displayed when processing is complete
+
+This architecture allows SciPaperLoader to handle CSV files with thousands of papers without timing out or blocking the web interface.
+
 ## Configuration
 
 Default configuration is loaded from `scipaperloader.defaults` and can be
 overriden by environment variables with a `FLASK_` prefix. See
 [Configuring from Environment Variables](https://flask.palletsprojects.com/en/3.0.x/config/#configuring-from-environment-variables).
 
+### Celery Configuration
+
+The following environment variables can be set to configure Celery:
+
+- `FLASK_CELERY_BROKER_URL`: Redis URL for the message broker (default: `redis://localhost:6379/0`)
+- `FLASK_CELERY_RESULT_BACKEND`: Redis URL for storing task results (default: `redis://localhost:6379/0`)
+
 Consider using
 [dotenv](https://flask.palletsprojects.com/en/3.0.x/cli/#environment-variables-from-dotenv).
 
@@ -58,4 +91,12 @@ deliver to your server, or copy in your `Dockerfile`, and insall it with `pip`.
 
 You must set a
 [SECRET_KEY](https://flask.palletsprojects.com/en/3.0.x/tutorial/deploy/#configure-the-secret-key)
-in production to a secret and stable value.
+in production to a secret and stable value.
+
+### Deploying with Celery
+
+When deploying to production:
+
+1. Configure a production-ready Redis instance or use a managed service
+2. Run Celery workers as system services or in Docker containers
+3. Consider setting up monitoring for your Celery tasks and workers

celery_worker.py

@@ -0,0 +1,7 @@
+from scipaperloader.celery import celery, configure_celery
+
+# Configure celery with Flask app
+configure_celery()
+
+if __name__ == '__main__':
+    celery.start()

pyproject.toml

@@ -13,6 +13,10 @@ dependencies = [
     "flask-wtf>=1.2.2,<2",
     "pyzotero>=1.6.11,<2",
     "pandas>=2.2.3,<3",
+    "celery>=5.5.1,<6",
+    "redis>=5.2.1,<6",
+    "flower>=2.0.1,<3",
+    "flask-migrate>=4.1.0,<5",
     ]
 
 [project.optional-dependencies]

scipaperloader/__init__.py

@@ -1,18 +1,24 @@
-from flask import Flask
-
+from flask import Flask, request
+from flask_migrate import Migrate  # Add this line
 from .config import Config
 from .db import db
 from .models import init_schedule_config
-
+from .models import ActivityLog, ActivityCategory
+from .blueprints import register_blueprints
 
 def create_app(test_config=None):
     app = Flask(__name__)
     app.config.from_object(Config)
 
+    # Celery configuration
+    app.config['CELERY_BROKER_URL'] = app.config.get('CELERY_BROKER_URL', 'redis://localhost:6379/0')
+    app.config['CELERY_RESULT_BACKEND'] = app.config.get('CELERY_RESULT_BACKEND', 'redis://localhost:6379/0')
+
     if test_config:
         app.config.update(test_config)
 
     db.init_app(app)
+    migrate = Migrate(app, db)  # Add this line to initialize Flask-Migrate
 
     with app.app_context():
         db.create_all()
@@ -22,8 +28,23 @@ def create_app(test_config=None):
     def inject_app_title():
         return {"app_title": app.config["APP_TITLE"]}
 
-    from . import views
+    register_blueprints(app)
 
-    app.register_blueprint(views.bp)
-
-    return app
+    @app.before_request
+    def before_request():
+        # Skip logging for static files, health checks, or other frequent requests
+        if request.path.startswith('/static/') or request.path == '/health' or request.path == '/favicon.ico':
+            return
+            
+        # Skip task status checks to avoid log spam
+        if request.path.startswith('/task_status/'):
+            return
+        
+        action = request.endpoint or request.path or "unknown_request"
+        ActivityLog.log_gui_interaction(
+            action=action,
+            description=f"Request to {request.path}",
+            extra={"method": request.method, "url": request.url}
+        )
+        
+    return app

scipaperloader/blueprints/__init__.py

@@ -0,0 +1,17 @@
+"""Blueprint registration module."""
+from flask import Flask
+
+from .main import bp as main_bp
+from .papers import bp as papers_bp
+from .upload import bp as upload_bp
+from .schedule import bp as schedule_bp
+from .logger import bp as logger_bp
+
+
+def register_blueprints(app: Flask):
+    """Register all blueprints with the Flask application."""
+    app.register_blueprint(main_bp)
+    app.register_blueprint(papers_bp, url_prefix='/papers')
+    app.register_blueprint(upload_bp, url_prefix='/upload')
+    app.register_blueprint(schedule_bp, url_prefix='/schedule')
+    app.register_blueprint(logger_bp, url_prefix='/logs')

scipaperloader/blueprints/logger.py

@@ -0,0 +1,112 @@
+"""Logger view."""
+import csv
+import io
+import datetime
+from flask import Blueprint, render_template, request, send_file
+from ..db import db
+from ..models import ActivityLog, ActivityCategory
+
+bp = Blueprint("logger", __name__, url_prefix="/logs")
+
+
+@bp.route("/")
+def list_logs():
+    page = request.args.get("page", 1, type=int)
+    per_page = 50
+
+    # Filters
+    category = request.args.get("category")
+    start_date = request.args.get("start_date")
+    end_date = request.args.get("end_date")
+    search_term = request.args.get("search_term")
+
+    if search_term == "None":
+        search_term = None
+
+
+    query = ActivityLog.query
+
+    if category:
+        query = query.filter(ActivityLog.category == category)
+    if start_date:
+        start_date_dt = datetime.datetime.strptime(start_date, "%Y-%m-%d")
+        query = query.filter(ActivityLog.timestamp >= start_date_dt)
+    if end_date:
+        end_date_dt = datetime.datetime.strptime(end_date, "%Y-%m-%d") + datetime.timedelta(days=1)
+        query = query.filter(ActivityLog.timestamp <= end_date_dt)
+    if search_term:
+        query = query.filter(db.or_(
+            ActivityLog.action.contains(search_term),
+            ActivityLog.description.contains(search_term)
+        ))
+
+    pagination = query.order_by(ActivityLog.timestamp.desc()).paginate(page=page, per_page=per_page, error_out=False)
+
+    categories = [e.value for e in ActivityCategory]
+
+    return render_template(
+        "logger.html.jinja",
+        logs=pagination.items,
+        pagination=pagination,
+        categories=categories,
+        category=category,
+        start_date=start_date,
+        end_date=end_date,
+        search_term=search_term,
+        app_title="PaperScraper",
+    )
+
+
+@bp.route("/download")
+def download_logs():
+    # Filters - reuse logic from list_logs
+    category = request.args.get("category")
+    start_date = request.args.get("start_date")
+    end_date = request.args.get("end_date")
+    search_term = request.args.get("search_term")
+
+    query = ActivityLog.query
+
+    if category:
+        query = query.filter(ActivityLog.category == category)
+    if start_date:
+        start_date_dt = datetime.datetime.strptime(start_date, "%Y-%m-%d")
+        query = query.filter(ActivityLog.timestamp >= start_date_dt)
+    if end_date:
+        end_date_dt = datetime.datetime.strptime(end_date, "%Y-%m-%d") + datetime.timedelta(days=1)
+        query = query.filter(ActivityLog.timestamp <= end_date_dt)
+    if search_term:
+        query = query.filter(db.or_(
+            ActivityLog.action.contains(search_term),
+            ActivityLog.description.contains(search_term)
+        ))
+
+    logs = query.order_by(ActivityLog.timestamp.desc()).all()
+
+    # Prepare CSV data
+    csv_data = io.StringIO()
+    csv_writer = csv.writer(csv_data)
+    csv_writer.writerow(["Timestamp", "Category", "Action", "Description", "Extra Data"])  # Header
+
+    for log in logs:
+        csv_writer.writerow([
+            log.timestamp,
+            log.category,
+            log.action,
+            log.description,
+            log.extra_data  # Consider formatting this better
+        ])
+
+    # Create response
+    filename = f"logs_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}.csv"
+    return send_file(
+        io.StringIO(csv_data.getvalue()),
+        mimetype="text/csv",
+        as_attachment=True,
+        download_name=filename
+    )
+
+@bp.route("/<int:log_id>/detail")
+def log_detail(log_id):
+    log = ActivityLog.query.get_or_404(log_id)
+    return render_template("partials/log_detail_modal.html.jinja", log=log)

scipaperloader/blueprints/main.py

@@ -0,0 +1,19 @@
+"""Main routes for the application."""
+from flask import Blueprint, render_template
+
+bp = Blueprint("main", __name__)
+
+
+@bp.route("/")
+def index():
+    return render_template("index.html.jinja")
+
+
+@bp.route("/logs")
+def logs():
+    return render_template("logs.html.jinja", app_title="PaperScraper")
+
+
+@bp.route("/about")
+def about():
+    return render_template("about.html.jinja", app_title="PaperScraper")

scipaperloader/blueprints/papers.py

@@ -0,0 +1,140 @@
+"""Paper management routes."""
+import csv
+import datetime
+import io
+
+from flask import (
+    Blueprint,
+    render_template,
+    request,
+    send_file,
+)
+from sqlalchemy import asc, desc
+
+from ..db import db
+from ..models import PaperMetadata
+
+bp = Blueprint("papers", __name__)
+
+
+@bp.route("/")
+def list_papers():
+    page = request.args.get("page", 1, type=int)
+    per_page = 50
+
+    # Filters
+    status = request.args.get("status")
+    created_from = request.args.get("created_from")
+    created_to = request.args.get("created_to")
+    updated_from = request.args.get("updated_from")
+    updated_to = request.args.get("updated_to")
+    sort_by = request.args.get("sort_by", "created_at")
+    sort_dir = request.args.get("sort_dir", "desc")
+
+    query = PaperMetadata.query
+
+    # Apply filters
+    if status:
+        query = query.filter(PaperMetadata.status == status)
+
+    def parse_date(val):
+        from datetime import datetime
+
+        try:
+            return datetime.strptime(val, "%Y-%m-%d")
+        except (ValueError, TypeError):
+            return None
+
+    if created_from := parse_date(created_from):
+        query = query.filter(PaperMetadata.created_at >= created_from)
+    if created_to := parse_date(created_to):
+        query = query.filter(PaperMetadata.created_at <= created_to)
+    if updated_from := parse_date(updated_from):
+        query = query.filter(PaperMetadata.updated_at >= updated_from)
+    if updated_to := parse_date(updated_to):
+        query = query.filter(PaperMetadata.updated_at <= updated_to)
+
+    # Sorting
+    sort_col = getattr(PaperMetadata, sort_by, PaperMetadata.created_at)
+    sort_func = desc if sort_dir == "desc" else asc
+    query = query.order_by(sort_func(sort_col))
+
+    # Pagination
+    pagination = query.paginate(page=page, per_page=per_page, error_out=False)
+
+    # Statistics
+    total_papers = PaperMetadata.query.count()
+    status_counts = (
+        db.session.query(PaperMetadata.status, db.func.count(PaperMetadata.status))
+        .group_by(PaperMetadata.status)
+        .all()
+    )
+    status_counts = {status: count for status, count in status_counts}
+
+    return render_template(
+        "papers.html.jinja",
+        papers=pagination.items,
+        pagination=pagination,
+        total_papers=total_papers,
+        status_counts=status_counts,
+        sort_by=sort_by,
+        sort_dir=sort_dir,
+    )
+
+
+@bp.route("/export")
+def export_papers():
+    # Filters
+    status = request.args.get("status")
+    created_from = request.args.get("created_from")
+    created_to = request.args.get("created_to")
+    updated_from = request.args.get("updated_from")
+    updated_to = request.args.get("updated_to")
+    sort_by = request.args.get("sort_by", "created_at")
+    sort_dir = request.args.get("sort_dir", "desc")
+
+    query = PaperMetadata.query
+
+    # Apply filters
+    if status:
+        query = query.filter(PaperMetadata.status == status)
+
+    def parse_date(val):
+        try:
+            return datetime.datetime.strptime(val, "%Y-%m-%d")
+        except Exception:
+            return None
+
+    output = io.StringIO()
+    writer = csv.writer(output)
+    writer.writerow(
+        ["ID", "Title", "Journal", "DOI", "ISSN", "Status", "Created At", "Updated At"]
+    )
+
+    for paper in query:
+        writer.writerow(
+            [
+                paper.id,
+                paper.title,
+                paper.journal,
+                paper.doi,
+                paper.issn,
+                paper.status,
+                paper.created_at,
+                paper.updated_at,
+            ]
+        )
+
+    output.seek(0)
+    return send_file(
+        io.BytesIO(output.read().encode("utf-8")),
+        mimetype="text/csv",
+        as_attachment=True,
+        download_name="papers.csv",
+    )
+
+
+@bp.route("/<int:paper_id>/detail")
+def paper_detail(paper_id):
+    paper = PaperMetadata.query.get_or_404(paper_id)
+    return render_template("partials/paper_detail_modal.html.jinja", paper=paper)

scipaperloader/blueprints/schedule.py

@@ -0,0 +1,79 @@
+"""Schedule configuration routes."""
+from flask import Blueprint, flash, render_template, request
+
+from ..db import db
+from ..models import ScheduleConfig, VolumeConfig
+
+bp = Blueprint("schedule", __name__)
+
+
+@bp.route("/", methods=["GET", "POST"])
+def schedule():
+    if request.method == "POST":
+        try:
+            # Check if we're updating volume or schedule
+            if "total_volume" in request.form:
+                # Volume update
+                try:
+                    new_volume = float(request.form.get("total_volume", 0))
+                    if new_volume <= 0 or new_volume > 1000:
+                        raise ValueError("Volume must be between 1 and 1000")
+
+                    volume_config = VolumeConfig.query.first()
+                    if not volume_config:
+                        volume_config = VolumeConfig(volume=new_volume)
+                        db.session.add(volume_config)
+                    else:
+                        volume_config.volume = new_volume
+
+                    db.session.commit()
+                    flash("Volume updated successfully!", "success")
+
+                except ValueError as e:
+                    db.session.rollback()
+                    flash(f"Error updating volume: {str(e)}", "error")
+            else:
+                # Schedule update logic
+                # Validate form data
+                for hour in range(24):
+                    key = f"hour_{hour}"
+                    if key not in request.form:
+                        raise ValueError(f"Missing data for hour {hour}")
+
+                    try:
+                        weight = float(request.form.get(key, 0))
+                        if weight < 0 or weight > 5:
+                            raise ValueError(
+                                f"Weight for hour {hour} must be between 0 and 5"
+                            )
+                    except ValueError:
+                        raise ValueError(f"Invalid weight value for hour {hour}")
+
+                # Update database if validation passes
+                for hour in range(24):
+                    key = f"hour_{hour}"
+                    weight = float(request.form.get(key, 0))
+                    config = ScheduleConfig.query.get(hour)
+                    if config:
+                        config.weight = weight
+                    else:
+                        db.session.add(ScheduleConfig(hour=hour, weight=weight))
+
+                db.session.commit()
+                flash("Schedule updated successfully!", "success")
+
+        except ValueError as e:
+            db.session.rollback()
+            flash(f"Error updating schedule: {str(e)}", "error")
+
+    schedule = {
+        sc.hour: sc.weight
+        for sc in ScheduleConfig.query.order_by(ScheduleConfig.hour).all()
+    }
+    volume = VolumeConfig.query.first()
+    return render_template(
+        "schedule.html.jinja",
+        schedule=schedule,
+        volume=volume.volume if volume else 0,
+        app_title="PaperScraper",
+    )

scipaperloader/blueprints/upload.py

@@ -0,0 +1,261 @@
+"""Upload functionality for paper metadata."""
+import codecs
+import csv
+import datetime
+from io import StringIO
+import json
+
+import pandas as pd
+from flask import (
+    Blueprint,
+    flash,
+    jsonify,
+    redirect,
+    render_template,
+    request,
+    send_file,
+    session,
+    url_for,
+    current_app
+)
+
+from ..db import db
+from ..models import PaperMetadata, ActivityLog
+from ..celery import celery  # Import the celery instance directly
+
+bp = Blueprint("upload", __name__)
+
+REQUIRED_COLUMNS = {"alternative_id", "journal", "doi", "issn", "title"}
+CHUNK_SIZE = 100  # Number of rows to process per batch
+
+def parse_date(date_str):
+    """Parse date string into datetime object."""
+    if not date_str or pd.isna(date_str):
+        return None
+    try:
+        return datetime.datetime.strptime(date_str, "%Y-%m-%d")
+    except ValueError:
+        return None
+
+@bp.route("/", methods=["GET", "POST"])
+def upload():
+    if request.method == "POST":
+        file = request.files.get("file")
+        delimiter = request.form.get("delimiter", ",")
+        duplicate_strategy = request.form.get("duplicate_strategy", "skip")
+
+        if not file:
+            return jsonify({"error": "No file selected."})
+
+        stream = codecs.iterdecode(file.stream, "utf-8")
+        content = "".join(stream)
+
+        # Trigger the Celery task
+        task = process_csv.delay(content, delimiter, duplicate_strategy)
+        
+        return jsonify({"task_id": task.id})
+
+    return render_template("upload.html.jinja")
+
+@celery.task(bind=True)
+def process_csv(self, file_content, delimiter, duplicate_strategy):
+    """Process CSV file and import paper metadata."""
+
+    # With the ContextTask in place, we're already inside an app context
+    added_count = skipped_count = updated_count = error_count = 0
+    errors = []
+    skipped_records = []  # Add this to track skipped records
+
+    try:
+        # Log the start of import using ActivityLog model
+        ActivityLog.log_import_activity(
+            action="start_csv_import",
+            status="processing",
+            description=f"Starting CSV import with strategy: {duplicate_strategy}",
+            file_size=len(file_content),
+            delimiter=delimiter
+        )
+
+        # Set initial progress percentage
+        self.update_state(state='PROGRESS', meta={'progress': 10})
+
+        # Read CSV into chunks
+        csv_buffer = StringIO(file_content)
+        # Count total chunks
+        csv_buffer.seek(0)
+        total_chunks = len(list(pd.read_csv(csv_buffer, delimiter=delimiter, chunksize=CHUNK_SIZE)))
+        csv_buffer.seek(0)
+
+        # Process each chunk of rows
+        for chunk_idx, chunk in enumerate(pd.read_csv(csv_buffer, delimiter=delimiter, chunksize=CHUNK_SIZE)):
+            for index, row in chunk.iterrows():
+                try:
+                    doi = str(row.get("doi", "N/A"))
+                    # Validate required fields
+                    if pd.isna(row.get("title")) or pd.isna(row.get("doi")) or pd.isna(row.get("issn")):
+                        raise ValueError("Missing required fields")
+
+                    # Try finding an existing record based on DOI
+                    existing = db.session.query(PaperMetadata).filter_by(doi=doi).first()
+                    if existing:
+                        if duplicate_strategy == "update":
+                            existing.title = row["title"]
+                            existing.alt_id = row.get("alternative_id")
+                            existing.issn = row["issn"]
+                            existing.journal = row.get("journal")
+                            existing.published_online = parse_date(row.get("published_online"))
+                            updated_count += 1
+                        else:
+                            # Track why this record was skipped
+                            skipped_records.append({
+                                "row": index + 2,
+                                "doi": doi,
+                                "reason": f"Duplicate DOI found and strategy is '{duplicate_strategy}'"
+                            })
+                            skipped_count += 1
+                            continue
+                    else:
+                        metadata = PaperMetadata(
+                            title=row["title"],
+                            doi=doi,
+                            alt_id=row.get("alternative_id"),
+                            issn=row["issn"],
+                            journal=row.get("journal"),
+                            published_online=parse_date(row.get("published_online")),
+                            status="New",
+                        )
+                        db.session.add(metadata)
+                        added_count += 1
+                except Exception as e:
+                    error_count += 1
+                    errors.append({"row": index + 2, "doi": row.get("doi", "N/A"), "error": str(e)})
+
+            # Commit the chunk and roll session fresh
+            db.session.commit()
+
+            # Log periodic progress every 5 chunks
+            if (chunk_idx + 1) % 5 == 0:
+                ActivityLog.log_import_activity(
+                    action="import_progress",
+                    status="processing",
+                    description=f"Processed {chunk_idx+1}/{total_chunks} chunks",
+                    current_stats={
+                        "added": added_count,
+                        "updated": updated_count,
+                        "skipped": skipped_count,
+                        "errors": error_count
+                    }
+                )
+
+            progress = min(90, 10 + int((chunk_idx + 1) * 80 / total_chunks))
+            self.update_state(state='PROGRESS', meta={'progress': progress})
+
+        # Final progress update and completion log
+        self.update_state(state='PROGRESS', meta={'progress': 100})
+        ActivityLog.log_import_activity(
+            action="complete_csv_import",
+            status="success",
+            description="CSV import completed",
+            stats={
+                "added": added_count,
+                "updated": updated_count,
+                "skipped": skipped_count,
+                "errors": error_count
+            }
+        )
+
+    except Exception as e:
+        db.session.rollback()
+        ActivityLog.log_error(
+            error_message="CSV import failed",
+            exception=e,
+            severity="error",
+            source="upload.process_csv"
+        )
+        return {'error': str(e), 'progress': 0}
+    finally:
+        db.session.remove()
+
+    # If there were errors, store an error CSV for potential download
+    if errors:
+        try:
+            error_csv = StringIO()
+            writer = csv.DictWriter(error_csv, fieldnames=["row", "doi", "error"])
+            writer.writeheader()
+            writer.writerows(errors)
+            ActivityLog.log_import_activity(
+                action="import_errors",
+                status="error",
+                description=f"Import completed with {error_count} errors",
+                error_csv=error_csv.getvalue(),
+                task_id=self.request.id,
+                error_count=error_count
+            )
+        except Exception:
+            # Do not fail the task if error logging fails
+            pass
+
+    # Update the return value to include skipped records information
+    return {
+        "added": added_count,
+        "updated": updated_count,
+        "skipped": skipped_count,
+        "skipped_records": skipped_records[:5],  # Include up to 5 examples
+        "skipped_reason_summary": "Records were skipped because they already exist in the database. Use 'update' strategy to update them.",
+        "errors": errors[:5],
+        "error_count": error_count,
+        "task_id": self.request.id
+    }
+    
+@bp.route("/task_status/<task_id>")
+def task_status(task_id):
+    """Get status of background task."""
+    task = celery.AsyncResult(task_id)
+    
+    if task.state == "PENDING":
+        response = {"state": task.state, "progress": 0}
+    elif task.state == "PROGRESS":
+        response = {
+            "state": task.state, 
+            "progress": task.info.get("progress", 0)
+        }
+    elif task.state == "SUCCESS":
+        response = {
+            "state": task.state,
+            "result": task.result
+        }
+    else:  # FAILURE, REVOKED, etc.
+        response = {
+            "state": task.state,
+            "error": str(task.info) if task.info else "Unknown error"
+        }
+    
+    return jsonify(response)
+
+@bp.route("/download_error_log/<task_id>")
+def download_error_log(task_id):
+    # Find the most recent error log for this task
+    error_log = ActivityLog.query.filter(
+        ActivityLog.action == "import_errors",
+        ActivityLog.extra_data.like(f'%"{task_id}"%')  # Search in JSON
+    ).order_by(ActivityLog.timestamp.desc()).first()
+    
+    if not error_log:
+        flash("No error data available.")
+        return redirect(url_for("upload.upload"))
+    
+    # Get the CSV data from extra_data
+    extra_data = error_log.get_extra_data()
+    error_csv = extra_data.get("error_csv")
+    
+    if not error_csv:
+        flash("Error data format is invalid.")
+        return redirect(url_for("upload.upload"))
+        
+    buffer = StringIO(error_csv)
+    return send_file(
+        buffer,
+        mimetype="text/csv",
+        as_attachment=True,
+        download_name=f"upload_errors_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}.csv"
+    )

scipaperloader/celery.py

@@ -0,0 +1,43 @@
+from celery import Celery
+
+# Create Celery instance without Flask app initially
+celery = Celery(
+    'scipaperloader',
+    broker='redis://localhost:6379/0',
+    backend='redis://localhost:6379/0',
+)
+
+def configure_celery(app=None):
+    """Configure Celery with the Flask app settings and ensure tasks run in the app context."""
+    if app is None:
+        # Import here to avoid circular import
+        from scipaperloader import create_app
+        app = create_app()
+
+    # Update Celery configuration using the app settings
+    celery.conf.update(
+        broker_url=app.config.get('CELERY_BROKER_URL', 'redis://localhost:6379/0'),
+        result_backend=app.config.get('CELERY_RESULT_BACKEND', 'redis://localhost:6379/0'),
+        task_serializer='json',
+        accept_content=['json'],
+        result_serializer='json',
+        timezone='UTC',
+        enable_utc=True,
+        task_time_limit=3600,         # 1 hour max runtime
+        task_soft_time_limit=3000,      # 50 minutes soft limit
+        worker_max_tasks_per_child=10,  # Restart workers after 10 tasks
+        worker_max_memory_per_child=1000000,  # 1GB memory limit
+        task_acks_late=True,            # Acknowledge tasks after completion
+        task_reject_on_worker_lost=True,  # Requeue tasks if worker dies
+    )
+
+    # Create a custom task class that pushes the Flask application context
+    class ContextTask(celery.Task):
+        abstract = True
+
+        def __call__(self, *args, **kwargs):
+            with app.app_context():
+                return self.run(*args, **kwargs)
+
+    celery.Task = ContextTask
+    return celery

scipaperloader/models.py

@@ -1,5 +1,184 @@
 from .db import db
 
+import json
+from datetime import datetime
+from enum import Enum
+
+
+class ActivityCategory(Enum):
+    """Categories for activity logs."""
+    GUI_INTERACTION = "gui_interaction"
+    CONFIG_CHANGE = "config_change"
+    SCRAPER_COMMAND = "scraper_command"
+    SCRAPER_ACTIVITY = "scraper_activity"
+    SYSTEM = "system"
+    DATA_IMPORT = "data_import"
+
+
+class ErrorSeverity(Enum):
+    """Severity levels for error logging."""
+    DEBUG = "debug"
+    INFO = "info"
+    WARNING = "warning"
+    ERROR = "error"
+    CRITICAL = "critical"
+
+
+class ActivityLog(db.Model):
+    """Model for logging various activities in the application."""
+    id = db.Column(db.Integer, primary_key=True)
+    timestamp = db.Column(db.DateTime, default=datetime.utcnow, index=True)
+    category = db.Column(db.String(50), nullable=False, index=True)
+    action = db.Column(db.String(100), nullable=False)
+    description = db.Column(db.Text)
+
+    # Reference to related entities (optional)
+    paper_id = db.Column(db.Integer, db.ForeignKey('paper_metadata.id'), nullable=True)
+    user_id = db.Column(db.Integer, nullable=True)  # For future authentication
+
+    # For config changes
+    config_key = db.Column(db.String(100), nullable=True)
+    old_value = db.Column(db.Text, nullable=True)
+    new_value = db.Column(db.Text, nullable=True)
+
+    # For scraper activities
+    status = db.Column(db.String(50), nullable=True)
+    source_ip = db.Column(db.String(50), nullable=True)
+
+    # Extra data as JSON
+    extra_data = db.Column(db.Text, nullable=True)
+
+    def set_extra_data(self, data_dict):
+        """Serialize extra data as JSON string."""
+        if data_dict:
+            self.extra_data = json.dumps(data_dict)
+
+    def get_extra_data(self):
+        """Deserialize JSON string to dictionary."""
+        if self.extra_data:
+            return json.loads(self.extra_data)
+        return {}
+
+    @classmethod
+    def log_gui_interaction(cls, action, description=None, paper_id=None, user_id=None, **extra):
+        """Log a GUI interaction."""
+        log = cls(
+            category=ActivityCategory.GUI_INTERACTION.value,
+            action=action,
+            description=description,
+            paper_id=paper_id,
+            user_id=user_id
+        )
+        log.set_extra_data(extra)
+        db.session.add(log)
+        db.session.commit()
+        return log
+
+    @classmethod
+    def log_config_change(cls, config_key, old_value, new_value, user_id=None, **extra):
+        """Log a configuration change."""
+        log = cls(
+            category=ActivityCategory.CONFIG_CHANGE.value,
+            action=f"Changed {config_key}",
+            config_key=config_key,
+            old_value=str(old_value),
+            new_value=str(new_value),
+            user_id=user_id
+        )
+        log.set_extra_data(extra)
+        db.session.add(log)
+        db.session.commit()
+        return log
+
+    @classmethod
+    def log_scraper_command(cls, action, status=None, user_id=None, **extra):
+        """Log a scraper command (start/stop/pause)."""
+        log = cls(
+            category=ActivityCategory.SCRAPER_COMMAND.value,
+            action=action,
+            status=status,
+            user_id=user_id
+        )
+        log.set_extra_data(extra)
+        db.session.add(log)
+        db.session.commit()
+        return log
+
+    @classmethod
+    def log_scraper_activity(cls, action, paper_id=None, status=None, description=None, **extra):
+        """Log a scraper activity (downloading, processing papers, etc.)."""
+        log = cls(
+            category=ActivityCategory.SCRAPER_ACTIVITY.value,
+            action=action,
+            paper_id=paper_id,
+            status=status,
+            description=description
+        )
+        log.set_extra_data(extra)
+        db.session.add(log)
+        db.session.commit()
+        return log
+
+    @classmethod
+    def log_error(cls, error_message, exception=None, severity=ErrorSeverity.ERROR.value,
+                  source=None, paper_id=None, user_id=None, **extra):
+        """Log system errors or warnings.
+
+        Args:
+            error_message: Brief description of the error
+            exception: The exception object if available
+            severity: Error severity level (debug, info, warning, error, critical)
+            source: Component/module where the error occurred
+            paper_id: Related paper ID if applicable
+            user_id: Related user ID if applicable
+            **extra: Any additional data to store
+        """
+        details = {}
+
+        if exception:
+            details.update({
+                'exception_type': type(exception).__name__,
+                'exception_message': str(exception)
+            })
+
+            # Get traceback if available
+            import traceback
+            details['traceback'] = traceback.format_exc()
+
+        if source:
+            extra['source'] = source
+
+        log = cls(
+            category=ActivityCategory.SYSTEM.value,
+            action=f"{severity.upper()}: {error_message}"[:100],  # Limit action length
+            description=error_message,
+            paper_id=paper_id,
+            user_id=user_id,
+            status=severity
+        )
+
+        # Add exception details to extra data
+        extra.update(details)
+        log.set_extra_data(extra)
+
+        db.session.add(log)
+        db.session.commit()
+        return log
+
+    @classmethod
+    def log_import_activity(cls, action, status=None, description=None, user_id=None, **extra):
+        """Log data import activities (CSV uploads, bulk imports, etc.)."""
+        log = cls(
+            category=ActivityCategory.DATA_IMPORT.value,
+            action=action,
+            status=status,
+            description=description,
+            user_id=user_id
+        )
+        log.set_extra_data(extra)
+        db.session.add(log)
+        db.session.commit()
+        return log
 
 class PaperMetadata(db.Model):
     id = db.Column(db.Integer, primary_key=True)
@@ -7,6 +186,7 @@ class PaperMetadata(db.Model):
     doi = db.Column(db.String, unique=True, index=True)
     alt_id = db.Column(db.String)
     issn = db.Column(db.String(32))
+    journal = db.Column(db.String(255))
     type = db.Column(db.String(50))
     language = db.Column(db.String(50))
     published_online = db.Column(db.Date)  # or DateTime/String
@@ -19,7 +199,6 @@ class PaperMetadata(db.Model):
         default=db.func.current_timestamp(),
         onupdate=db.func.current_timestamp(),
     )
-    # plus maybe timestamps for created/updated
 
 
 class ScheduleConfig(db.Model):

scipaperloader/static/styles.css

@@ -1,5 +1,9 @@
 .message {
-    padding: 10px;
-    font-size: 1.3em;
-    font-family: Arial, sans-serif;
+  padding: 10px;
+  font-size: 1.3em;
+  font-family: Arial, sans-serif;
+}
+
+.progress-bar {
+  width: 0%;
 }

scipaperloader/templates/about.html.jinja

@@ -1,4 +1,4 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html.jinja" %} {% block content %}
 <h1 class="mb-4">📘 About This App</h1>
 
 <p class="lead">
@@ -107,4 +107,4 @@
     <li>Anyone needing a structured way to fetch and track papers in bulk</li>
   </ul>
 </section>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/base.html

@@ -1,22 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta charset="UTF-8" />
-    <title>{{ app_title }}</title>
-    <link
-      href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css"
-      rel="stylesheet"
-    />
-    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
-    <!-- Optional Alpine.js -->
-    <script
-      defer
-      src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"
-    ></script>
-  </head>
-  <body>
-    {% include 'nav.html' %}
-    <main class="container my-5">{% block content %}{% endblock %}</main>
-    {% include 'footer.html' %}
-  </body>
-</html>

scipaperloader/templates/base.html.jinja

@@ -0,0 +1,21 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+  <meta charset="UTF-8" />
+  <meta name="description" content="A platform to load scientific papers and manage metadata." />
+  <meta name="keywords" content="science, papers, research, management" />
+  <title>{{ app_title }}</title>
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet" />
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+  <!-- Optional Alpine.js -->
+  <script defer src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"></script>
+</head>
+
+<body>
+  {% include "nav.html.jinja" %}
+  <main class="container my-5">{% block content %}{% endblock content %}</main>
+  {% include "footer.html.jinja" %}
+</body>
+
+</html>

scipaperloader/templates/index.html.jinja

@@ -1,4 +1,5 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html.jinja" %}
+{% block content %}
 
 <div class="container text-center">
   <h1 class="display-4">Welcome to SciPaperLoader</h1>
@@ -16,7 +17,7 @@
           (title, DOI, ISSN, etc.) are stored. Errors are reported without
           aborting the batch.
         </p>
-        <a href="/import" class="btn btn-sm btn-outline-primary">Upload Now</a>
+        <a href="{{ url_for('upload.upload') }}" class="btn btn-sm btn-outline-primary">Upload Now</a>
       </div>
     </div>
   </div>
@@ -29,7 +30,7 @@
           A daemon process runs hourly to fetch papers using Zotero API.
           Downloads are randomized to mimic human behavior and avoid detection.
         </p>
-        <a href="/logs" class="btn btn-sm btn-outline-secondary">View Logs</a>
+        <a href="{{ url_for('logger.list_logs') }}" class="btn btn-sm btn-outline-secondary">View Logs</a>
       </div>
     </div>
   </div>
@@ -43,9 +44,7 @@
           inspect errors. Files are stored on disk in structured folders per
           DOI.
         </p>
-        <a href="/papers" class="btn btn-sm btn-outline-success"
-          >Browse Papers</a
-        >
+        <a href="{{ url_for('papers.list_papers') }}" class="btn btn-sm btn-outline-success">Browse Papers</a>
       </div>
     </div>
   </div>
@@ -59,11 +58,9 @@
           volume (e.g. 2/hour at daytime, 0 at night) to match your bandwidth or
           usage pattern.
         </p>
-        <a href="/schedule" class="btn btn-sm btn-outline-warning"
-          >Adjust Schedule</a
-        >
+        <a href="{{ url_for('schedule.schedule') }}" class="btn btn-sm btn-outline-warning">Adjust Schedule</a>
       </div>
     </div>
   </div>
 </div>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/logger.html.jinja

@@ -0,0 +1,117 @@
+{% extends "base.html.jinja" %}
+{% block content %}
+<h1>Activity Logs</h1>
+
+<form method="get" class="mb-3">
+  <div class="row g-2">
+    <div class="col-md-3">
+      <label for="category" class="form-label">Category:</label>
+      <select name="category" id="category" class="form-select">
+        <option value="">All</option>
+        {% for cat in categories %}
+        <option value="{{ cat }}" {% if category==cat %}selected{% endif %}>{{ cat }}</option>
+        {% endfor %}
+      </select>
+    </div>
+
+    <div class="col-md-3">
+      <label for="start_date" class="form-label">Start Date:</label>
+      <input type="date" name="start_date" id="start_date" value="{{ start_date }}" class="form-control">
+    </div>
+
+    <div class="col-md-3">
+      <label for="end_date" class="form-label">End Date:</label>
+      <input type="date" name="end_date" id="end_date" value="{{ end_date }}" class="form-control">
+    </div>
+
+    <div class="col-md-3">
+      <label for="search_term" class="form-label">Search:</label>
+      <input type="text" name="search_term" id="search_term" value="{{ search_term }}" class="form-control">
+    </div>
+  </div>
+
+  <div class="mt-3">
+    <button type="submit" class="btn btn-primary">Filter</button>
+    <a href="{{ url_for('logger.download_logs', category=category, start_date=start_date, end_date=end_date, search_term=search_term) }}"
+      class="btn btn-secondary">Download CSV</a>
+  </div>
+</form>
+
+<ul class="list-group">
+  {% for log in logs %}
+  <li class="list-group-item log-item" data-log-id="{{ log.id }}">
+    <div class="d-flex justify-content-between align-items-center">
+      <div class="ms-2 me-auto">
+        <div class="fw-bold">{{ log.timestamp }}</div>
+        {{ log.action }} - {{ log.description }}
+      </div>
+      <span class="badge bg-primary rounded-pill">{{ log.category }}</span>
+    </div>
+  </li>
+  {% endfor %}
+</ul>
+
+{% if pagination %}
+<nav aria-label="Page navigation" class="mt-4">
+  <ul class="pagination justify-content-center">
+    {% if pagination.has_prev %}
+    <li class="page-item">
+      <a class="page-link"
+        href="{{ url_for('logger.list_logs', page=pagination.prev_num, category=category, start_date=start_date, end_date=end_date, search_term=search_term) }}">Previous</a>
+    </li>
+    {% else %}
+    <li class="page-item disabled">
+      <span class="page-link">Previous</span>
+    </li>
+    {% endif %}
+
+    <li class="page-item disabled">
+      <span class="page-link">Page {{ pagination.page }} of {{ pagination.pages }}</span>
+    </li>
+
+    {% if pagination.has_next %}
+    <li class="page-item">
+      <a class="page-link"
+        href="{{ url_for('logger.list_logs', page=pagination.next_num, category=category, start_date=start_date, end_date=end_date, search_term=search_term) }}">Next</a>
+    </li>
+    {% else %}
+    <li class="page-item disabled">
+      <span class="page-link">Next</span>
+    </li>
+    {% endif %}
+  </ul>
+</nav>
+{% endif %}
+
+<!-- Modal for log details -->
+<div class="modal fade" id="logDetailModal" tabindex="-1" aria-hidden="true">
+  <div class="modal-dialog modal-lg modal-dialog-scrollable">
+    <div class="modal-content" id="log-detail-content">
+      <!-- Log details will be loaded here via AJAX -->
+    </div>
+  </div>
+</div>
+
+<script>
+  document.addEventListener("DOMContentLoaded", function () {
+    const modal = new bootstrap.Modal(document.getElementById('logDetailModal'));
+    const content = document.getElementById('log-detail-content');
+
+    document.querySelectorAll('.log-item').forEach(item => {
+      item.addEventListener('click', function () {
+        const logId = this.getAttribute('data-log-id');
+        fetch(`/logs/${logId}/detail`)
+          .then(response => response.text())
+          .then(html => {
+            content.innerHTML = html;
+            modal.show();
+          })
+          .catch(err => {
+            content.innerHTML = '<div class="modal-body text-danger">Error loading log details.</div>';
+            modal.show();
+          });
+      });
+    });
+  });
+</script>
+{% endblock content %}

scipaperloader/templates/nav.html

@@ -1,63 +0,0 @@
-<nav class="navbar navbar-expand-lg navbar-light bg-light">
-  <div class="container-fluid">
-    <a class="navbar-brand" href="{{ url_for('main.index') }}"
-      >{{ app_title }}</a
-    >
-    <button
-      class="navbar-toggler"
-      type="button"
-      data-bs-toggle="collapse"
-      data-bs-target="#navbarSupportedContent"
-      aria-controls="navbarSupportedContent"
-      aria-expanded="false"
-      aria-label="Toggle navigation"
-    >
-      <span class="navbar-toggler-icon"></span>
-    </button>
-    <div class="collapse navbar-collapse" id="navbarSupportedContent">
-      <ul class="navbar-nav me-auto mb-2 mb-lg-0">
-        <li class="nav-item">
-          <a class="nav-link" href="/upload">Import CSV</a>
-        </li>
-        <li class="nav-item">
-            <a class="nav-link" href="/papers">Papers</a>
-        </li>
-        <li class="nav-item">
-          <a class="nav-link" href="/schedule">Schedule</a>
-        </li>
-        <li class="nav-item dropdown">
-          <a
-            class="nav-link dropdown-toggle"
-            href="#"
-            id="navbarDropdown"
-            role="button"
-            data-bs-toggle="dropdown"
-            aria-expanded="false"
-          >
-            More
-          </a>
-          <ul class="dropdown-menu" aria-labelledby="navbarDropdown">
-            <li>
-                <a class="dropdown-item" href="/logs">Logs</a>
-            </li>
-            <li>
-                <a class="dropdown-item" href="/about">About</a>
-            </li>
-            <li>
-              <a class="dropdown-item" href="https://git.mbeck.cologne">Help</a>
-            </li>
-          </ul>
-        </li>
-      </ul>
-      <form class="d-flex">
-        <input
-          class="form-control me-2"
-          type="search"
-          placeholder="Search"
-          aria-label="Search"
-        />
-        <button class="btn btn-outline-success" type="submit">Search</button>
-      </form>
-    </div>
-  </div>
-</nav>

scipaperloader/templates/nav.html.jinja

@@ -0,0 +1,43 @@
+<nav class="navbar navbar-expand-lg navbar-light bg-light">
+  <div class="container-fluid">
+    <a class="navbar-brand" href="{{ url_for('main.index') }}">{{ app_title }}</a>
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent"
+      aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+    <div class="collapse navbar-collapse" id="navbarSupportedContent">
+      <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+        <li class="nav-item">
+          <a class="nav-link" href="{{ url_for('upload.upload') }}">Import CSV</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="{{ url_for('papers.list_papers') }}">Papers</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="{{ url_for('schedule.schedule') }}">Schedule</a>
+        </li>
+        <li class="nav-item dropdown">
+          <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-bs-toggle="dropdown"
+            aria-expanded="false">
+            More
+          </a>
+          <ul class="dropdown-menu" aria-labelledby="navbarDropdown">
+            <li>
+              <a class="dropdown-item" href="{{ url_for('logger.list_logs') }}">Logs</a>
+            </li>
+            <li>
+              <a class="dropdown-item" href="{{ url_for('main.about') }}">About</a>
+            </li>
+            <li>
+              <a class="dropdown-item" href="https://git.mbeck.cologne">Help</a>
+            </li>
+          </ul>
+        </li>
+      </ul>
+      <form class="d-flex">
+        <input class="form-control me-2" type="search" placeholder="Search" aria-label="Search" />
+        <button class="btn btn-outline-success" type="submit">Search</button>
+      </form>
+    </div>
+  </div>
+</nav>

scipaperloader/templates/papers.html

@@ -1,258 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Papers{% endblock %}
-{% block content %}
-
-{# --- Sort direction logic for each column --- #}
-{% set title_sort = 'asc' if sort_by != 'title' or sort_dir == 'desc' else 'desc' %}
-{% set journal_sort = 'asc' if sort_by != 'journal' or sort_dir == 'desc' else 'desc' %}
-{% set doi_sort = 'asc' if sort_by != 'doi' or sort_dir == 'desc' else 'desc' %}
-{% set issn_sort = 'asc' if sort_by != 'issn' or sort_dir == 'desc' else 'desc' %}
-{% set status_sort = 'asc' if sort_by != 'status' or sort_dir == 'desc' else 'desc' %}
-{% set created_sort = 'asc' if sort_by != 'created_at' or sort_dir == 'desc' else 'desc' %}
-{% set updated_sort = 'asc' if sort_by != 'updated_at' or sort_dir == 'desc' else 'desc' %}
-
-<form method="get" class="mb-4 row g-3">
-    <div class="col-md-2">
-        <label>Status</label>
-        <select name="status" class="form-select">
-            <option value="">All</option>
-            {% if request.args.get('status') == 'Pending' %}
-                <option value="Pending" selected>Pending</option>
-            {% else %}
-                <option value="Pending">Pending</option>
-            {% endif %}
-            
-            {% if request.args.get('status') == 'Done' %}
-                <option value="Done" selected>Done</option>
-            {% else %}
-                <option value="Done">Done</option>
-            {% endif %}
-            
-            {% if request.args.get('status') == 'Failed' %}
-                <option value="Failed" selected>Failed</option>
-            {% else %}
-                <option value="Failed">Failed</option>
-            {% endif %}
-        </select>
-    </div>
-    <div class="col-md-2">
-        <label>Created from</label>
-        <input type="date" name="created_from" class="form-control" value="{{ request.args.get('created_from', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Created to</label>
-        <input type="date" name="created_to" class="form-control" value="{{ request.args.get('created_to', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Updated from</label>
-        <input type="date" name="updated_from" class="form-control" value="{{ request.args.get('updated_from', '') }}">
-    </div>
-    <div class="col-md-2">
-        <label>Updated to</label>
-        <input type="date" name="updated_to" class="form-control" value="{{ request.args.get('updated_to', '') }}">
-    </div>
-    <div class="col-md-2 d-flex align-items-end">
-        <button type="submit" class="btn btn-primary w-100">Filter</button>
-    </div>
-</form>
-
-<div class="modal fade" id="paperDetailModal" tabindex="-1" aria-hidden="true">
-    <div class="modal-dialog modal-lg modal-dialog-scrollable">
-        <div class="modal-content" id="paper-detail-content">
-            <!-- AJAX-loaded content will go here -->
-        </div>
-    </div>
-</div>
-
-<div class="d-flex align-items-center mb-4">
-    <!-- Statistics Section -->
-    <div class="me-auto">
-        <div class="list-group list-group-horizontal">
-            <div class="list-group-item d-flex justify-content-between align-items-center">
-                <strong>Total Papers</strong>
-                <span class="badge bg-primary rounded-pill">{{ total_papers }}</span>
-            </div>
-            {% for status, count in status_counts.items() %}
-                <div class="list-group-item d-flex justify-content-between align-items-center">
-                    <strong>{{ status }}:</strong>
-                    <span class="badge bg-primary rounded-pill">{{ count }}</span>
-                </div>
-            {% endfor %}
-        </div>
-    </div>
-
-    <!-- Pagination Section -->
-    <nav aria-label="Page navigation" class="mx-auto">
-        <ul class="pagination justify-content-center mb-0">
-            {% if pagination.has_prev %}
-            <li class="page-item">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('main.list_papers', page=pagination.prev_num, **params) }}" aria-label="Previous">
-                    <span aria-hidden="true">&laquo;</span>
-                </a>
-            </li>
-            {% else %}
-            <li class="page-item disabled">
-                <span class="page-link" aria-hidden="true">&laquo;</span>
-            </li>
-            {% endif %}
-
-            {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
-            {% if page_num %}
-            <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('main.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
-            </li>
-            {% else %}
-            <li class="page-item disabled"><span class="page-link">…</span></li>
-            {% endif %}
-            {% endfor %}
-
-            {% if pagination.has_next %}
-            <li class="page-item">
-                {% set params = request.args.to_dict() %}
-                {% set _ = params.pop('page', None) %}
-                <a class="page-link" href="{{ url_for('main.list_papers', page=pagination.next_num, **params) }}" aria-label="Next">
-                    <span aria-hidden="true">&raquo;</span>
-                </a>
-            </li>
-            {% else %}
-            <li class="page-item disabled">
-                <span class="page-link" aria-hidden="true">&raquo;</span>
-            </li>
-            {% endif %}
-        </ul>
-    </nav>
-
-    <!-- Buttons Section -->
-    <div class="ms-auto">
-        <a href="{{ url_for('main.export_papers') }}" class="btn btn-outline-secondary">Export CSV</a>
-    </div>
-</div>
-    <table class="table table-striped table-bordered table-smaller">
-        <thead>
-            <tr>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'title', 'sort_dir': title_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">Title</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'journal', 'sort_dir': journal_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">Journal</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'doi', 'sort_dir': doi_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">DOI</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'issn', 'sort_dir': issn_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">ISSN</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'status', 'sort_dir': status_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">Status</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'created_at', 'sort_dir': created_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">Created</a>
-                </th>
-                <th>
-                    {% set params = request.args.to_dict() %}
-                    {% set params = params.update({'sort_by': 'updated_at', 'sort_dir': updated_sort}) or params %}
-                    <a href="{{ url_for('main.list_papers', **params) }}">Updated</a>
-                </th>
-            </tr>
-        </thead>
-        <tbody>
-            {% for paper in papers %}
-            <tr>
-                <td><a href="#" class="paper-link" data-url="{{ url_for('main.paper_detail', paper_id=paper.id) }}">{{ paper.title }}</a></td>
-                <td>{{ paper.journal }}</td>
-                <td>{{ paper.doi }}</td>
-                <td>{{ paper.issn }}</td>
-                <td>{{ paper.status }}</td>
-                <td>{{ paper.created_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
-                <td>{{ paper.updated_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
-            </tr>
-            {% endfor %}
-        </tbody>
-    </table>
-</div>
-
-<nav aria-label="Page navigation">
-    <ul class="pagination justify-content-center">
-        {% if pagination.has_prev %}
-        <li class="page-item">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('main.list_papers', page=pagination.prev_num, **params) }}" aria-label="Previous">
-                <span aria-hidden="true">&laquo;</span>
-            </a>
-        </li>
-        {% else %}
-        <li class="page-item disabled">
-            <span class="page-link" aria-hidden="true">&laquo;</span>
-        </li>
-        {% endif %}
-
-        {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
-        {% if page_num %}
-        <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('main.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
-        </li>
-        {% else %}
-        <li class="page-item disabled"><span class="page-link">…</span></li>
-        {% endif %}
-        {% endfor %}
-
-        {% if pagination.has_next %}
-        <li class="page-item">
-            {% set params = request.args.to_dict() %}
-            {% set _ = params.pop('page', None) %}
-            <a class="page-link" href="{{ url_for('main.list_papers', page=pagination.next_num, **params) }}" aria-label="Next">
-                <span aria-hidden="true">&raquo;</span>
-            </a>
-        </li>
-        {% else %}
-        <li class="page-item disabled">
-            <span class="page-link" aria-hidden="true">&raquo;</span>
-        </li>
-        {% endif %}
-    </ul>
-</nav>
-
-<script>
-document.addEventListener("DOMContentLoaded", function () {
-    const modal = new bootstrap.Modal(document.getElementById('paperDetailModal'));
-    const content = document.getElementById('paper-detail-content');
-
-    document.querySelectorAll('.paper-link').forEach(link => {
-        link.addEventListener('click', function (e) {
-            e.preventDefault();
-            const url = this.getAttribute('data-url');
-
-            fetch(url)
-                .then(response => response.text())
-                .then(html => {
-                    content.innerHTML = html;
-                    modal.show();
-                })
-                .catch(err => {
-                    content.innerHTML = '<div class="modal-body text-danger">Error loading details.</div>';
-                    modal.show();
-                });
-        });
-    });
-});
-</script>
-{% endblock %}

scipaperloader/templates/papers.html.jinja

@@ -0,0 +1,281 @@
+{% extends "base.html.jinja" %}
+{% block title %}Papers{% endblock title %}
+{% block content %}
+
+{# --- Sort direction logic for each column --- #}
+{% set title_sort = 'asc' if sort_by != 'title' or sort_dir == 'desc' else 'desc' %}
+{% set journal_sort = 'asc' if sort_by != 'journal' or sort_dir == 'desc' else 'desc' %}
+{% set doi_sort = 'asc' if sort_by != 'doi' or sort_dir == 'desc' else 'desc' %}
+{% set issn_sort = 'asc' if sort_by != 'issn' or sort_dir == 'desc' else 'desc' %}
+{% set status_sort = 'asc' if sort_by != 'status' or sort_dir == 'desc' else 'desc' %}
+{% set created_sort = 'asc' if sort_by != 'created_at' or sort_dir == 'desc' else 'desc' %}
+{% set updated_sort = 'asc' if sort_by != 'updated_at' or sort_dir == 'desc' else 'desc' %}
+
+<form method="get" class="mb-4 row g-3">
+    <div class="col-md-2">
+        <label>Status</label>
+        <select name="status" class="form-select">
+            <option value="">All</option>
+            {% if request.args.get('status') == 'Pending' %}
+            <option value="Pending" selected>Pending</option>
+            {% else %}
+            <option value="Pending">Pending</option>
+            {% endif %}
+
+            {% if request.args.get('status') == 'Done' %}
+            <option value="Done" selected>Done</option>
+            {% else %}
+            <option value="Done">Done</option>
+            {% endif %}
+
+            {% if request.args.get('status') == 'Failed' %}
+            <option value="Failed" selected>Failed</option>
+            {% else %}
+            <option value="Failed">Failed</option>
+            {% endif %}
+        </select>
+    </div>
+    <div class="col-md-2">
+        <label>Created from</label>
+        <input type="date" name="created_from" class="form-control" value="{{ request.args.get('created_from', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Created to</label>
+        <input type="date" name="created_to" class="form-control" value="{{ request.args.get('created_to', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Updated from</label>
+        <input type="date" name="updated_from" class="form-control" value="{{ request.args.get('updated_from', '') }}">
+    </div>
+    <div class="col-md-2">
+        <label>Updated to</label>
+        <input type="date" name="updated_to" class="form-control" value="{{ request.args.get('updated_to', '') }}">
+    </div>
+    <div class="col-md-2 d-flex align-items-end">
+        <button type="submit" class="btn btn-primary w-100">Filter</button>
+    </div>
+</form>
+
+<div class="modal fade" id="paperDetailModal" tabindex="-1" aria-hidden="true">
+    <div class="modal-dialog modal-lg modal-dialog-scrollable">
+        <div class="modal-content" id="paper-detail-content">
+            <!-- AJAX-loaded content will go here -->
+        </div>
+    </div>
+</div>
+
+<div class="d-flex align-items-center mb-4">
+    <!-- Statistics Section -->
+    <div class="me-auto">
+        <div class="list-group list-group-horizontal">
+            <div class="list-group-item d-flex justify-content-between align-items-center">
+                <strong>Total Papers</strong>
+                <span class="badge bg-primary rounded-pill">{{ total_papers }}</span>
+            </div>
+            {% for status, count in status_counts.items() %}
+            <div class="list-group-item d-flex justify-content-between align-items-center">
+                <strong>{{ status }}:</strong>
+                <span class="badge bg-primary rounded-pill">{{ count }}</span>
+            </div>
+            {% endfor %}
+        </div>
+    </div>
+
+    <!-- Pagination Section -->
+    <nav aria-label="Page navigation" class="mx-auto">
+        <ul class="pagination justify-content-center mb-0">
+            {% if pagination.has_prev %}
+            <li class="page-item">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}"
+                    aria-label="Previous">
+                    <span aria-hidden="true">«</span>
+                </a>
+            </li>
+            {% else %}
+            <li class="page-item disabled">
+                <span class="page-link" aria-hidden="true">«</span>
+            </li>
+            {% endif %}
+
+            {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
+            {% if page_num %}
+            <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num
+                    }}</a>
+            </li>
+            {% else %}
+            <li class="page-item disabled"><span class="page-link">…</span></li>
+            {% endif %}
+            {% endfor %}
+
+            {% if pagination.has_next %}
+            <li class="page-item">
+                {% set params = request.args.to_dict() %}
+                {% set _ = params.pop('page', None) %}
+                <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}"
+                    aria-label="Next">
+                    <span aria-hidden="true">»</span>
+                </a>
+            </li>
+            {% else %}
+            <li class="page-item disabled">
+                <span class="page-link" aria-hidden="true">»</span>
+            </li>
+            {% endif %}
+        </ul>
+    </nav>
+
+    <!-- Buttons Section -->
+    <div class="ms-auto">
+        <a href="{{ url_for('papers.export_papers') }}" class="btn btn-outline-secondary">Export CSV</a>
+    </div>
+</div>
+<table class="table table-striped table-bordered table-smaller">
+    <thead>
+        <tr>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'title', 'sort_dir': title_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Title</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'journal', 'sort_dir': journal_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Journal</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'doi', 'sort_dir': doi_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">DOI</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'issn', 'sort_dir': issn_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">ISSN</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'status', 'sort_dir': status_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Status</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'created_at', 'sort_dir': created_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Created</a>
+            </th>
+            <th>
+                {% set params = request.args.to_dict() %}
+                {% set params = params.update({'sort_by': 'updated_at', 'sort_dir': updated_sort}) or params %}
+                <a href="{{ url_for('papers.list_papers', **params) }}">Updated</a>
+            </th>
+        </tr>
+    </thead>
+    <tbody>
+        {% for paper in papers %}
+        <tr>
+            <td>
+                <a href="#" class="icon-link icon-link-hover paper-link"
+                    data-url="{{ url_for('papers.paper_detail', paper_id=paper.id) }}">
+                    <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
+                        <path
+                            d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z" />
+                        <path
+                            d="M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z" />
+                    </svg>
+                    {{ paper.title }}
+                </a>
+            </td>
+            <td>{{ paper.journal }}</td>
+            <td>
+                <a href="https://doi.org/{{ paper.doi }}" target="_blank" class="icon-link icon-link-hover">
+                    {{ paper.doi }}
+                    <svg xmlns="http://www.w3.org/2000/svg" class="bi" viewBox="0 0 16 16" aria-hidden="true">
+                        <path
+                            d="M1 8a.5.5 0 0 1 .5-.5h11.793l-3.147-3.146a.5.5 0 0 1 .708-.708l4 4a.5.5 0 0 1 0 .708l-4 4a.5.5 0 0 1-.708-.708L13.293 8.5H1.5A.5.5 0 0 1 1 8z" />
+                    </svg>
+                </a>
+            </td>
+            <td>{{ paper.issn }}</td>
+            <td>{{ paper.status }}</td>
+            <td>{{ paper.created_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
+            <td>{{ paper.updated_at.strftime('%Y-%m-%d %H:%M:%S') }}</td>
+        </tr>
+        {% endfor %}
+    </tbody>
+</table>
+
+<nav aria-label="Page navigation">
+    <ul class="pagination justify-content-center">
+        {% if pagination.has_prev %}
+        <li class="page-item">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.prev_num, **params) }}"
+                aria-label="Previous">
+                <span aria-hidden="true">«</span>
+            </a>
+        </li>
+        {% else %}
+        <li class="page-item disabled">
+            <span class="page-link" aria-hidden="true">«</span>
+        </li>
+        {% endif %}
+
+        {% for page_num in pagination.iter_pages(left_edge=2, right_edge=2, left_current=2, right_current=2) %}
+        {% if page_num %}
+        <li class="page-item {% if page_num == pagination.page %}active{% endif %}">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=page_num, **params) }}">{{ page_num }}</a>
+        </li>
+        {% else %}
+        <li class="page-item disabled"><span class="page-link">…</span></li>
+        {% endif %}
+        {% endfor %}
+
+        {% if pagination.has_next %}
+        <li class="page-item">
+            {% set params = request.args.to_dict() %}
+            {% set _ = params.pop('page', None) %}
+            <a class="page-link" href="{{ url_for('papers.list_papers', page=pagination.next_num, **params) }}"
+                aria-label="Next">
+                <span aria-hidden="true">»</span>
+            </a>
+        </li>
+        {% else %}
+        <li class="page-item disabled">
+            <span class="page-link" aria-hidden="true">»</span>
+        </li>
+        {% endif %}
+    </ul>
+</nav>
+
+<script>
+    document.addEventListener("DOMContentLoaded", function () {
+        const modal = new bootstrap.Modal(document.getElementById('paperDetailModal'));
+        const content = document.getElementById('paper-detail-content');
+
+        document.querySelectorAll('.paper-link').forEach(link => {
+            link.addEventListener('click', function (e) {
+                e.preventDefault();
+                const url = this.getAttribute('data-url');
+
+                fetch(url)
+                    .then(response => response.text())
+                    .then(html => {
+                        content.innerHTML = html;
+                        modal.show();
+                    })
+                    .catch(err => {
+                        content.innerHTML = '<div class="modal-body text-danger">Error loading details.</div>';
+                        modal.show();
+                    });
+            });
+        });
+    });
+</script>
+{% endblock content %}

scipaperloader/templates/partials/log_detail_modal.html.jinja

@@ -0,0 +1,18 @@
+<div class="modal-header">
+  <h5 class="modal-title">Log Details</h5>
+  <button type="button" class="btn-close" data-bs-dismiss="modal"></button>
+</div>
+<div class="modal-body">
+  <p><strong>Timestamp:</strong> {{ log.timestamp }}</p>
+  <p><strong>Category:</strong> {{ log.category }}</p>
+  <p><strong>Action:</strong> {{ log.action }}</p>
+  <p><strong>Description:</strong> {{ log.description }}</p>
+  {% if log.extra_data %}
+  <p><strong>Extra Data:</strong>
+  <pre><code>{{ log.extra_data }}</code></pre>
+  </p>
+  {% endif %}
+</div>
+<div class="modal-footer">
+  <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+</div>

scipaperloader/templates/partials/paper_detail_modal.html

@@ -1,14 +0,0 @@
-<div class="modal-header">
-    <h5 class="modal-title">{{ paper.title }}</h5>
-    <button type="button" class="btn-close" data-bs-dismiss="modal"></button>
-</div>
-<div class="modal-body">
-    {% for key, value in paper.__dict__.items() %}
-        {% if not key.startswith('_') and key != 'metadata' %}
-            <p><strong>{{ key.replace('_', ' ').capitalize() }}:</strong> {{ value }}</p>
-        {% endif %}
-    {% endfor %}
-</div>
-<div class="modal-footer">
-    <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
-</div>

scipaperloader/templates/partials/paper_detail_modal.html.jinja

@@ -0,0 +1,32 @@
+<div class="modal-header">
+  <h5 class="modal-title">{{ paper.title }}</h5>
+  <button type="button" class="btn-close" data-bs-dismiss="modal"></button>
+</div>
+<div class="modal-body">
+  {% for key, value in paper.__dict__.items() %} {% if key == 'doi' %}
+  <p>
+    <strong>DOI:</strong>
+    <a href="https://doi.org/{{ value }}" target="_blank">{{ value }}</a>
+  </p>
+  {% elif key == 'issn' %} {% if ',' in value %}
+  <p>
+    <strong>ISSN:</strong>
+    {% for issn in value.split(',') %}
+    <a href="https://www.worldcat.org/search?q=issn:{{ issn.strip() }}" target="_blank">{{ issn.strip() }}</a>{% if not
+    loop.last %}, {% endif %} {% endfor %}
+  </p>
+  {% else %}
+  <p>
+    <strong>ISSN:</strong>
+    <a href="https://www.worldcat.org/search?q=issn:{{ value }}" target="_blank">{{ value }}</a>
+  </p>
+  {% endif %} {% endif %} {% if not key.startswith('_') and key != 'metadata'
+  and key != 'doi' and key != 'issn' %}
+  <p><strong>{{ key.replace('_', ' ').capitalize() }}:</strong> {{ value }}</p>
+  {% endif %} {% endfor %}
+</div>
+<div class="modal-footer">
+  <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">
+    Close
+  </button>
+</div>

scipaperloader/templates/schedule.html.jinja

@@ -1,15 +1,17 @@
-{% extends 'base.html' %} {% block content %}
+{% extends "base.html.jinja" %} {% block content %}
 <style>
   .timeline {
     display: flex;
     flex-wrap: wrap;
     gap: 3px;
-    user-select: none; /* Prevent text selection during drag */
+    user-select: none;
+    /* Prevent text selection during drag */
   }
 
   .hour-block {
     width: 49px;
-    height: 70px; /* Increased height to fit additional text */
+    height: 70px;
+    /* Increased height to fit additional text */
     border-radius: 5px;
     text-align: center;
     line-height: 1.2;
@@ -76,11 +78,8 @@
   messages %}
   <div id="flash-messages">
     {% for category, message in messages %}
-    <div
-      class="flash-message {{ category }}"
-      x-data="{}"
-      x-init="setTimeout(() => $el.classList.add('fade'), 100); setTimeout(() => $el.remove(), 5000)"
-    >
+    <div class="flash-message {{ category }}" x-data="{}"
+      x-init="setTimeout(() => $el.classList.add('fade'), 100); setTimeout(() => $el.remove(), 5000)">
       {{ message }}
     </div>
     {% endfor %}
@@ -118,39 +117,21 @@
       <strong x-text="volume"></strong> papers.
     </p>
     <div class="d-flex align-items-center mb-3">
-      <form
-        method="POST"
-        action="{{ url_for('main.schedule') }}"
-        class="input-group w-50"
-      >
+      <form method="post" action="{{ url_for('schedule.schedule') }}" class="input-group w-50">
         <label class="input-group-text">Papers per day:</label>
-        <input
-          type="number"
-          class="form-control"
-          name="total_volume"
-          value="{{ volume }}"
-          min="1"
-          max="1000"
-          required
-        />
+        <input type="number" class="form-control" name="total_volume" value="{{ volume }}" min="1" max="1000"
+          required />
         <button type="submit" class="btn btn-primary">Update Volume</button>
       </form>
     </div>
   </div>
 
   <h2 class="mt-4">Current Schedule</h2>
-  <form method="POST" action="{{ url_for('main.schedule') }}">
+  <form method="post" action="{{ url_for('schedule.schedule') }}">
     <div class="timeline mb-3" @mouseup="endDrag()" @mouseleave="endDrag()">
       <template x-for="hour in Object.keys(schedule)" :key="hour">
-        <div
-          class="hour-block"
-          :id="'hour-' + hour"
-          :data-hour="hour"
-          :style="getBackgroundStyle(hour)"
-          :class="{'selected': isSelected(hour)}"
-          @mousedown="startDrag($event, hour)"
-          @mouseover="dragSelect(hour)"
-        >
+        <div class="hour-block" :id="'hour-' + hour" :data-hour="hour" :style="getBackgroundStyle(hour)"
+          :class="{'selected': isSelected(hour)}" @mousedown="startDrag($event, hour)" @mouseover="dragSelect(hour)">
           <div><strong x-text="formatHour(hour)"></strong></div>
           <div class="weight"><span x-text="schedule[hour]"></span></div>
           <div class="papers">
@@ -163,25 +144,14 @@
 
     <div class="input-group mb-4 w-50">
       <label class="input-group-text">Set Weight:</label>
-      <input
-        type="number"
-        step="0.1"
-        min="0"
-        max="5"
-        x-model="newWeight"
-        class="form-control"
-      />
-      <button
-        type="button"
-        class="btn btn-outline-primary"
-        @click="applyWeight()"
-      >
+      <input type="number" step="0.1" min="0" max="5" x-model="newWeight" class="form-control" />
+      <button type="button" class="btn btn-outline-primary" @click="applyWeight()">
         Apply to Selected
       </button>
     </div>
 
     <div class="d-flex justify-content-between">
-      <a href="/" class="btn btn-outline-secondary">⬅ Back</a>
+      <a href="{{ url_for('main.index') }}" class="btn btn-outline-secondary">⬅ Back</a>
       <button type="submit" class="btn btn-success">💾 Save Schedule</button>
     </div>
   </form>
@@ -297,4 +267,4 @@
     };
   }
 </script>
-{% endblock %}
+{% endblock content %}

scipaperloader/templates/upload.html

@@ -1,73 +0,0 @@
-{% extends 'base.html' %}
-{% block content %}
-<h1>Welcome to SciPaperLoader</h1>
-
-{% if success %}
-    <div class="alert alert-success mt-3">{{ success }}</div>
-{% endif %}
-
-{% if error_message %}
-    <div class="alert alert-warning mt-3">
-        <h4>{{ error_message }}</h4>
-        <table class="table table-sm table-bordered">
-            <thead>
-                <tr>
-                    <th>Row</th>
-                    <th>DOI</th>
-                    <th>Error</th>
-                </tr>
-            </thead>
-            <tbody>
-                {% for error in error_samples %}
-                <tr>
-                    <td>{{ error.row }}</td>
-                    <td>{{ error.doi }}</td>
-                    <td>{{ error.error }}</td>
-                </tr>
-                {% endfor %}
-            </tbody>
-        </table>
-        <a href="{{ url_for('main.download_error_log') }}" class="btn btn-outline-secondary">Download Full Error Log</a>
-    </div>
-{% endif %}
-
-<div class="alert alert-info">
-    <p><strong>Instructions:</strong> Please upload a CSV file containing academic paper metadata. The file must include the following columns:</p>
-    <ul>
-        <li><code>alternative_id</code> – an alternative title or abbreviation</li>
-        <li><code>journal</code> – the journal name</li>
-        <li><code>doi</code> – the digital object identifier</li>
-        <li><code>issn</code> – the ISSN of the journal</li>
-        <li><code>title</code> – the title of the paper</li>
-    </ul>
-    <p>The format of your CSV should resemble the response structure of the Crossref API's <code>/journals/{issn}/works</code> endpoint.</p>
-</div>
-
-<form method="POST" action="{{ url_for('main.upload') }}" enctype="multipart/form-data">
-    <div class="mb-3">
-        <label class="form-label">How to handle duplicate DOIs:</label>
-        <div class="form-check">
-            <input class="form-check-input" type="radio" name="duplicate_strategy" value="skip" id="skip" checked>
-            <label class="form-check-label" for="skip">Skip duplicate entries</label>
-        </div>
-        <div class="form-check">
-            <input class="form-check-input" type="radio" name="duplicate_strategy" value="update" id="update">
-            <label class="form-check-label" for="update">Update existing entries</label>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="file">Upload CSV File</label>
-        <input type="file" name="file" id="file" class="form-control" required>
-    </div>
-    <div class="form-group mt-3">
-        <label for="delimiter">Choose CSV Delimiter</label>
-        <select name="delimiter" id="delimiter" class="form-control">
-            <option value=",">Comma (,)</option>
-            <option value=";">Semicolon (;)</option>
-            <option value="\t">Tab (\\t)</option>
-            <option value="|">Pipe (|)</option>
-        </select>
-    </div>
-    <button type="submit" class="btn btn-primary mt-3">Upload</button>
-</form>
-{% endblock %}

scipaperloader/templates/upload.html.jinja

@@ -0,0 +1,234 @@
+{% extends "base.html.jinja" %} {% block content %}
+<h1>Welcome to SciPaperLoader</h1>
+
+<div id="results-container"></div>
+
+{% if success %}
+<div class="alert alert-success mt-3">{{ success }}</div>
+{% endif %} {% if error_message %}
+<div class="alert alert-warning mt-3">
+  <h4>{{ error_message }}</h4>
+  <table class="table table-sm table-bordered">
+    <thead>
+      <tr>
+        <th>Row</th>
+        <th>DOI</th>
+        <th>Error</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for error in error_samples %}
+      <tr>
+        <td>{{ error.row }}</td>
+        <td>{{ error.doi }}</td>
+        <td>{{ error.error }}</td>
+      </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+  <a href="{{ url_for('upload.download_error_log') }}" class="btn btn-outline-secondary">Download Full Error Log</a>
+</div>
+{% endif %}
+
+<div class="alert alert-info">
+  <p>
+    <strong>Instructions:</strong> Please upload a CSV file containing academic
+    paper metadata. The file must include the following columns:
+  </p>
+  <ul>
+    <li><code>alternative_id</code> – an alternative title or abbreviation</li>
+    <li><code>journal</code> – the journal name</li>
+    <li><code>doi</code> – the digital object identifier</li>
+    <li><code>issn</code> – the ISSN of the journal</li>
+    <li><code>title</code> – the title of the paper</li>
+  </ul>
+</div>
+
+<form method="post" action="{{ url_for('upload.upload') }}" enctype="multipart/form-data" id="upload-form">
+  <div class="form-group">
+    <label for="file">Upload CSV File</label>
+    <input type="file" name="file" id="file" class="form-control" required />
+  </div>
+  <div class="form-group mt-3">
+    <label for="delimiter">Choose CSV Delimiter</label>
+    <select name="delimiter" id="delimiter" class="form-control">
+      <option value=",">Comma (,)</option>
+      <option value=";">Semicolon (;)</option>
+      <option value="\t">Tab (\\t)</option>
+      <option value="|">Pipe (|)</option>
+    </select>
+  </div>
+  <button type="submit" class="btn btn-primary mt-3">Upload</button>
+</form>
+
+<!-- Progress Modal -->
+<div id="progressModal" class="modal fade" tabindex="-1">
+  <div class="modal-dialog">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Processing Your Upload</h5>
+      </div>
+      <div class="modal-body">
+        <div class="progress">
+          <div id="progressBar" class="progress-bar" role="progressbar">0%</div>
+        </div>
+        <p id="progressStatus" class="mt-2 text-center">Starting...</p>
+      </div>
+    </div>
+  </div>
+</div>
+
+<script>
+  const form = document.getElementById("upload-form");
+  form.addEventListener("submit", function (e) {
+    e.preventDefault();
+
+    // Display loading state immediately
+    const progressModal = new bootstrap.Modal(document.getElementById("progressModal"));
+    progressModal.show();
+    const progressBar = document.getElementById("progressBar");
+    progressBar.style.width = "5%";
+    progressBar.textContent = "Starting...";
+
+    const formData = new FormData(form);
+
+    // Disable the form while processing
+    const submitButton = form.querySelector("button[type='submit']");
+    submitButton.disabled = true;
+
+    fetch(form.action, {
+      method: "POST",
+      body: formData,
+    })
+      .then((response) => response.json())
+      .then((data) => {
+        if (data.error) {
+          // Handle error
+          progressModal.hide();
+          alert(`Error: ${data.error}`);
+          submitButton.disabled = false;
+          return;
+        }
+
+        const taskId = data.task_id;
+        const interval = setInterval(() => {
+          fetch("{{ url_for('upload.task_status', task_id='') }}" + taskId)
+            .then((response) => response.json())
+            .then((status) => {
+              console.log("Task status:", status);
+              if (status.state === "SUCCESS") {
+                clearInterval(interval);
+                progressBar.style.width = "100%";
+                progressBar.textContent = "Completed!";
+
+                setTimeout(() => {
+                  progressModal.hide();
+                  showResults(status.result);
+                  submitButton.disabled = false;
+                }, 1000);
+              } else if (status.state === "FAILURE") {
+                clearInterval(interval);
+                progressBar.style.width = "100%";
+                progressBar.classList.add("bg-danger");
+                progressBar.textContent = "Failed!";
+
+                setTimeout(() => {
+                  progressModal.hide();
+                  alert(`Task failed: ${status.error || "Unknown error"}`);
+                  submitButton.disabled = false;
+                }, 1000);
+              } else {
+                // Update progress bar with more information
+                const progress = status.progress || 0;
+                progressBar.style.width = `${progress}%`;
+                progressBar.textContent = `${progress}% complete`;
+                document.getElementById("progressStatus").innerText = `Processing... (${status.state})`;
+              }
+            })
+            .catch((err) => {
+              console.error("Failed to check task status:", err);
+            });
+        }, 1000);
+      })
+      .catch((err) => {
+        console.error("Upload failed:", err);
+        progressModal.hide();
+        alert("Upload failed. Please try again.");
+        submitButton.disabled = false;
+      });
+  });
+
+  const showResults = (result) => {
+    const message = `Upload completed! Added: ${result.added}, Updated: ${result.updated}, Skipped: ${result.skipped}, Errors: ${result.error_count}`;
+
+    let resultHTML = `<div class="alert alert-success">${message}</div>`;
+
+    // Add skipped records information
+    if (result.skipped > 0) {
+      resultHTML += `
+        <div class="alert alert-info">
+          <h4>${result.skipped} records were skipped</h4>
+          <p>${result.skipped_reason_summary || "Records were skipped because they already exist in the database."}</p>
+          ${result.skipped_records && result.skipped_records.length > 0 ? `
+            <p>Examples of skipped records:</p>
+            <table class="table table-sm table-bordered">
+              <thead>
+                <tr>
+                  <th>Row</th>
+                  <th>DOI</th>
+                  <th>Reason</th>
+                </tr>
+              </thead>
+              <tbody>
+                ${result.skipped_records.map(record => `
+                  <tr>
+                    <td>${record.row}</td>
+                    <td>${record.doi}</td>
+                    <td>${record.reason}</td>
+                  </tr>
+                `).join('')}
+              </tbody>
+            </table>
+          ` : ''}
+        </div>`;
+    }
+
+    // Existing error display code
+    if (result.error_count > 0) {
+      resultHTML += `
+        <div class="alert alert-warning">
+          <h4>Some errors occurred (${result.error_count} total)</h4>
+          <p>Showing first ${result.errors.length} of ${result.error_count} errors:</p>
+          <table class="table table-sm table-bordered">
+            <thead>
+              <tr>
+                <th>Row</th>
+                <th>DOI</th>
+                <th>Error</th>
+              </tr>
+            </thead>
+            <tbody>`;
+
+      result.errors.forEach(error => {
+        resultHTML += `
+          <tr>
+            <td>${error.row}</td>
+            <td>${error.doi}</td>
+            <td>${error.error}</td>
+          </tr>`;
+      });
+
+      resultHTML += `
+            </tbody>
+          </table>
+          <p class="mt-2">Download the complete error log with all ${result.error_count} errors:</p>
+          <a href="/upload/download_error_log/${result.task_id}" class="btn btn-outline-secondary">
+            Download Full Error Log
+          </a>
+        </div>`;
+    }
+
+    document.getElementById("results-container").innerHTML = resultHTML;
+  };
+</script>
+{% endblock content %}

scipaperloader/views.py

@@ -1,389 +0,0 @@
-import codecs
-import csv
-import datetime
-import io
-from io import StringIO
-
-import pandas as pd
-from flask import (
-    Blueprint,
-    current_app,
-    flash,
-    redirect,
-    render_template,
-    request,
-    send_file,
-    session,  # Add this line
-    url_for,
-)
-
-from sqlalchemy import asc, desc
-
-from .db import db
-from .models import PaperMetadata, ScheduleConfig, VolumeConfig
-
-bp = Blueprint("main", __name__)
-
-
-@bp.route("/")
-def index():
-    return render_template("index.html")
-
-
-REQUIRED_COLUMNS = {"alternative_id", "journal", "doi", "issn", "title"}
-
-
-@bp.route("/upload", methods=["GET", "POST"])
-def upload():
-    if request.method == "POST":
-        file = request.files.get("file")
-        delimiter = request.form.get("delimiter", ",")
-        duplicate_strategy = request.form.get("duplicate_strategy", "skip")
-
-        if not file:
-            return render_template("upload.html", error="No file selected.")
-
-        try:
-            stream = codecs.iterdecode(file.stream, "utf-8")
-            content = "".join(stream)
-            df = pd.read_csv(StringIO(content), delimiter=delimiter)
-        except Exception as e:
-            return render_template("upload.html", error=f"Failed to read CSV file: {e}")
-
-        missing = REQUIRED_COLUMNS - set(df.columns)
-        if missing:
-            return render_template(
-                "upload.html", error=f"Missing required columns: {', '.join(missing)}"
-            )
-
-        # Optional: parse 'published_online' to date
-        def parse_date(val):
-            if pd.isna(val):
-                return None
-            try:
-                return pd.to_datetime(val).date()
-            except Exception:
-                return None
-
-        # Count statistics
-        added_count = 0
-        skipped_count = 0
-        updated_count = 0
-        error_count = 0
-        
-        # Collect error information
-        errors = []
-        
-        # Process each row
-        for index, row in df.iterrows():
-            try:
-                # Get DOI from row for error reporting
-                doi = str(row.get("doi", "N/A"))
-                
-                # Validate required fields
-                for field in ["title", "doi", "issn"]:
-                    if pd.isna(row.get(field)) or not str(row.get(field)).strip():
-                        raise ValueError(f"Missing required field: {field}")
-                
-                # Check if paper with this DOI already exists
-                existing = PaperMetadata.query.filter_by(doi=doi).first()
-                
-                if existing:
-                    if duplicate_strategy == 'update':
-                        # Update existing record
-                        existing.title = row["title"]
-                        existing.alt_id = row.get("alternative_id")
-                        existing.issn = row["issn"]
-                        existing.journal = row.get("journal")
-                        existing.type = row.get("type")
-                        existing.language = row.get("language")
-                        existing.published_online = parse_date(row.get("published_online"))
-                        updated_count += 1
-                    else:
-                        # Skip this record
-                        skipped_count += 1
-                        continue
-                else:
-                    # Create new record
-                    metadata = PaperMetadata(
-                        title=row["title"],
-                        doi=doi,
-                        alt_id=row.get("alternative_id"),
-                        issn=row["issn"],
-                        journal=row.get("journal"),
-                        type=row.get("type"),
-                        language=row.get("language"),
-                        published_online=parse_date(row.get("published_online")),
-                        status="New",
-                        file_path=None,
-                        error_msg=None,
-                    )
-                    db.session.add(metadata)
-                    added_count += 1
-                    
-            except Exception as e:
-                error_count += 1
-                errors.append({
-                    "row": index + 2,  # +2 because index is 0-based and we have a header row
-                    "doi": row.get("doi", "N/A"),
-                    "error": str(e)
-                })
-                continue  # Skip this row and continue with the next
-
-        try:
-            db.session.commit()
-        except Exception as e:
-            db.session.rollback()
-            return render_template(
-                "upload.html", error=f"Failed to save data to database: {e}"
-            )
-
-        # Prepare error samples for display
-        error_samples = errors[:5] if errors else []
-        
-        error_message = None
-        if errors:
-            error_message = f"Encountered {len(errors)} errors. First 5 shown below."
-            
-        # Store the full errors list in the session for potential download
-        if errors:
-            error_csv = StringIO()
-            writer = csv.DictWriter(error_csv, fieldnames=["row", "doi", "error"])
-            writer.writeheader()
-            writer.writerows(errors)
-            session["error_data"] = error_csv.getvalue()
-
-        return render_template(
-            "upload.html", 
-            success=f"File processed! Added: {added_count}, Updated: {updated_count}, Skipped: {skipped_count}, Errors: {error_count}",
-            error_message=error_message,
-            error_samples=error_samples
-        )
-
-    return render_template("upload.html")
-
-# Add a route to download the error log
-@bp.route("/download_error_log")
-def download_error_log():
-    error_data = session.get("error_data")
-    if not error_data:
-        flash("No error data available.")
-        return redirect(url_for("main.upload"))
-        
-    buffer = StringIO(error_data)
-    return send_file(
-        buffer,
-        mimetype="text/csv",
-        as_attachment=True,
-        download_name=f"upload_errors_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}.csv"
-    )
-    
-
-@bp.route("/papers")
-def list_papers():
-    page = request.args.get("page", 1, type=int)
-    per_page = 50
-
-    # Filters
-    status = request.args.get("status")
-    created_from = request.args.get("created_from")
-    created_to = request.args.get("created_to")
-    updated_from = request.args.get("updated_from")
-    updated_to = request.args.get("updated_to")
-    sort_by = request.args.get("sort_by", "created_at")
-    sort_dir = request.args.get("sort_dir", "desc")
-
-    query = PaperMetadata.query
-
-    # Apply filters
-    if status:
-        query = query.filter(PaperMetadata.status == status)
-
-    def parse_date(val):
-        from datetime import datetime
-
-        try:
-            return datetime.strptime(val, "%Y-%m-%d")
-        except (ValueError, TypeError):
-            return None
-
-    if created_from := parse_date(created_from):
-        query = query.filter(PaperMetadata.created_at >= created_from)
-    if created_to := parse_date(created_to):
-        query = query.filter(PaperMetadata.created_at <= created_to)
-    if updated_from := parse_date(updated_from):
-        query = query.filter(PaperMetadata.updated_at >= updated_from)
-    if updated_to := parse_date(updated_to):
-        query = query.filter(PaperMetadata.updated_at <= updated_to)
-
-    # Sorting
-    sort_col = getattr(PaperMetadata, sort_by, PaperMetadata.created_at)
-    sort_func = desc if sort_dir == "desc" else asc
-    query = query.order_by(sort_func(sort_col))
-
-    # Pagination
-    pagination = query.paginate(page=page, per_page=per_page, error_out=False)
-
-    # Statistics
-    total_papers = PaperMetadata.query.count()
-    status_counts = (
-        db.session.query(PaperMetadata.status, db.func.count(PaperMetadata.status))
-        .group_by(PaperMetadata.status)
-        .all()
-    )
-    status_counts = {status: count for status, count in status_counts}
-
-    return render_template(
-        "papers.html",
-        papers=pagination.items,
-        pagination=pagination,
-        total_papers=total_papers,
-        status_counts=status_counts,
-        sort_by=sort_by,
-        sort_dir=sort_dir,
-    )
-
-
-@bp.route("/papers/export")
-def export_papers():
-    query = PaperMetadata.query
-
-    # Filters
-    status = request.args.get("status")
-    created_from = request.args.get("created_from")
-    created_to = request.args.get("created_to")
-    updated_from = request.args.get("updated_from")
-    updated_to = request.args.get("updated_to")
-    sort_by = request.args.get("sort_by", "created_at")
-    sort_dir = request.args.get("sort_dir", "desc")
-
-    query = PaperMetadata.query
-
-    # Apply filters
-    if status:
-        query = query.filter(PaperMetadata.status == status)
-
-    def parse_date(val):
-        try:
-            return datetime.datetime.strptime(val, "%Y-%m-%d")
-        except Exception:
-            return None
-
-    output = io.StringIO()
-    writer = csv.writer(output)
-    writer.writerow(
-        ["ID", "Title", "Journal", "DOI", "ISSN", "Status", "Created At", "Updated At"]
-    )
-
-    for paper in query:
-        writer.writerow(
-            [
-                paper.id,
-                paper.title,
-                getattr(paper, "journal", ""),
-                paper.doi,
-                paper.issn,
-                paper.status,
-                paper.created_at,
-                paper.updated_at,
-            ]
-        )
-
-    output.seek(0)
-    return send_file(
-        io.BytesIO(output.read().encode("utf-8")),
-        mimetype="text/csv",
-        as_attachment=True,
-        download_name="papers.csv",
-    )
-
-
-
-
-@bp.route("/papers/<int:paper_id>/detail")
-def paper_detail(paper_id):
-    paper = PaperMetadata.query.get_or_404(paper_id)
-
-    return render_template("partials/paper_detail_modal.html", paper=paper)
-
-
-@bp.route("/schedule", methods=["GET", "POST"])
-def schedule():
-    if request.method == "POST":
-        try:
-            # Check if we're updating volume or schedule
-            if "total_volume" in request.form:
-                # Volume update
-                try:
-                    new_volume = float(request.form.get("total_volume", 0))
-                    if new_volume <= 0 or new_volume > 1000:
-                        raise ValueError("Volume must be between 1 and 1000")
-
-                    volume_config = VolumeConfig.query.first()
-                    if not volume_config:
-                        volume_config = VolumeConfig(volume=new_volume)
-                        db.session.add(volume_config)
-                    else:
-                        volume_config.volume = new_volume
-
-                    db.session.commit()
-                    flash("Volume updated successfully!", "success")
-
-                except ValueError as e:
-                    db.session.rollback()
-                    flash(f"Error updating volume: {str(e)}", "error")
-            else:
-                # Schedule update logic
-                # Validate form data
-                for hour in range(24):
-                    key = f"hour_{hour}"
-                    if key not in request.form:
-                        raise ValueError(f"Missing data for hour {hour}")
-
-                    try:
-                        weight = float(request.form.get(key, 0))
-                        if weight < 0 or weight > 5:
-                            raise ValueError(
-                                f"Weight for hour {hour} must be between 0 and 5"
-                            )
-                    except ValueError:
-                        raise ValueError(f"Invalid weight value for hour {hour}")
-
-                # Update database if validation passes
-                for hour in range(24):
-                    key = f"hour_{hour}"
-                    weight = float(request.form.get(key, 0))
-                    config = ScheduleConfig.query.get(hour)
-                    if config:
-                        config.weight = weight
-                    else:
-                        db.session.add(ScheduleConfig(hour=hour, weight=weight))
-
-                db.session.commit()
-                flash("Schedule updated successfully!", "success")
-
-        except ValueError as e:
-            db.session.rollback()
-            flash(f"Error updating schedule: {str(e)}", "error")
-
-    schedule = {
-        sc.hour: sc.weight
-        for sc in ScheduleConfig.query.order_by(ScheduleConfig.hour).all()
-    }
-    volume = VolumeConfig.query.first()
-    return render_template(
-        "schedule.html",
-        schedule=schedule,
-        volume=volume.volume,
-        app_title="PaperScraper",
-    )
-
-
-@bp.route("/logs")
-def logs():
-    return render_template("logs.html", app_title="PaperScraper")
-
-
-@bp.route("/about")
-def about():
-    return render_template("about.html", app_title="PaperScraper")